---
title: "Cereal Blast Tracker "
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    source_code: embed
  
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)

library(flexdashboard)
library(prettydoc)
library(readxl)
library(tidyverse)
library(crosstalk)
library(plotly)
library(viridis)
library(gsheet)
library(leaflet.providers)
```



```{r load data, message=FALSE, warning=FALSE, include=FALSE}
Sys.setlocale("LC_ALL", "pt_BR.UTF-8")


mg_prod <- gsheet2tbl("https://docs.google.com/spreadsheets/d/13xAflAQ-x78Vkq0O0jUEkUxHPq5G1R4gwqzillMxoTo/edit?usp=sharing")

wb1 <- gsheet2tbl("https://docs.google.com/spreadsheets/d/1iYPjVBNXqwrNwp0lQI2YZnUChfSjVn3b5guuxnYS144/edit?usp=sharing")
wb_all <- wb1 %>%
  
  filter(sample != 0) %>%
  filter(region != "UNEMAT") %>%
  mutate(id = case_when(
    is.na(species) ~ "No",
    TRUE ~ "Yes"
  )) %>%
  mutate(wheat = case_when(
    host == "Triticum aestivum" ~ "Wheat",
    TRUE ~ "Non-wheat")) %>% 
    dplyr::select(code, sample, lat, long, host, city, date, year, PstI_specie, species, wheat, DNA_extraction)    

set.seed(1000)
wb_all$lat <- round(jitter(wb_all$lat, factor = 1, amount = 0.02), 4)
wb_all$long <- round(jitter(wb_all$long, factor = 1, amount = 0.02), 4)

wb_grass <- wb1 %>%
  filter(sample != 0) %>%
  filter(region != "UNEMAT") %>%
  mutate(id = case_when(
    is.na(species) ~ "No",
    TRUE ~ "Yes"
  )) %>%
  filter(host == "Eleusine indica" | host == "Panicum maximum" | host == "Urochloa brizantha" | host == "Rhynchelytrum roseum" | host == "Urochloa humidicola" | host == "Urochloa plantaginea" | host == "Cynodon plectostachyus") %>%
  mutate(host2 = case_when(
    host == "Urochloa brizantha" ~ "Urochloa spp.",
    host == "Urochloa humidicola" ~ "Urochloa spp.",
    host == "Urochloa plantaginea" ~ "Urochloa spp.",
    TRUE ~ host
  ))

set.seed(1000)
wb_grass$lat <- round(jitter(wb_grass$lat, factor = 1, amount = 0.01), 4)
wb_grass$long <- round(jitter(wb_grass$long, factor = 1, amount = 0.01), 4)
```



```{r all table, echo=FALSE}
library(crosstalk)
library(leaflet)
library(leaflet.extras)
library(DT)
sd <- SharedData$new(wb_all)
sd_grass <- SharedData$new(wb_grass)
```


Inputs {.sidebar}
-------------------------------------



### Quick filter


```{r}
#filter_slider("year", "Select years", sd, ~year)
filter_select("host", "Select host", sd, ~host)
filter_select("PstI_specie", "Pyricularia spp.", sd, ~PstI_specie)
filter_checkbox("DNA_extraction", "DNA extraction", sd, ~DNA_extraction, inline = TRUE)
filter_checkbox("wheat", "Host group", sd, ~wheat, inline = TRUE)


```


Row {data-height=300}
-------------------------------------


### Plot host species


```{r}
sd %>% 
  plot_ly(x = ~ wheat,
          color = ~wheat, 
          colors = "Set2") %>% 
  layout(barmode = 'stack',
         margin=list(l=20,r=20,t=20,b=20)) 



```




###  All hosts

```{r}
library(RColorBrewer)
library(htmltools)
pal <- colorFactor("Set2", domain = c("Wheat", "Non-wheat"))

leaflet(data = sd) %>%
  setView(-47.96101, -19.72314, zoom = 5) %>%
  addProviderTiles(providers$CartoDB.Voyager) %>%
  addCircleMarkers(
    group = "wheat",
    radius = 6,
    fillOpacity = 1,
    weight = 0.5,
    label = paste(wb_all$host, "- Details"),
    fillColor = ~ pal(wheat),
    popup = paste(
      "Code:", wb_all$"code", "", "
",
      "Field sample:", wb_all$"sample", "", "
",
      "Host:", wb_all$"host", "", "
",
      "Tissue:", wb_all$"tissue", "", "
",
      "Field sample:", wb_all$"sample", "", "
",
      "City:", wb_all$"city", "", "
",
      "Year:", wb_all$"year", "", "
",
      "DNA extraction:", wb_all$"DNA_extraction", "", "
",
      "Species:", wb_all$"PstI_specie", "", "
",
      "OBS:", wb_all$"observation", "", "
"
    )
  ) %>%
  addLegend("bottomleft",
    pal = pal,
    values = ~wheat,
    title = "Host",
    opacity = 1
  ) %>%
  addEasyButton(easyButton(
    icon = "fa-globe", title = "Back to initial view",
    onClick = JS("function(btn, map){ map.setZoom(2); }")
  ))
```


Row
----------


###  Grid display


```{r}
datatable(sd,
  extensions = c("Buttons", "ColReorder"),
  escape = TRUE, rownames = FALSE,
  class = "cell-border stripe",
  options = list(
    dom = "Bfrtip", buttons = c("excel", "pdf"), deferRender = TRUE,
    scrollY = 50,
    pageLength = 15,
    scroller = TRUE,
    colReorder = TRUE
  )
)
```